Apologies - I was trying to explain as clearly as possible, but have obviously failed! ;) Anyway, this goes back to a previous writeup for finding microsatellites in genome files. Having solved the problem of finding them I now need to count them and sort them into categories, viz.

• Which genome file they were found in ($b).
• How long the repeating motif is, e.g. 3 units ($c).
• What the repeating motif is, e.g. ATT ($d).
• How many repeating motifs there are, e.g.(ATT)6 ($e).

There are various outputs I need, but the first would be a file for each genome showing each unique motif ($d) and how many of them were found for a particular length, e.g.

units|A|AT|GT|ATT|...etc.
11   |1|0 |2 |3  |...
12   |0|1 |1 |4  |...

This shows that I've found one case of an A that is 11 units long, no ATs of the same number of units, but two GTs of 11 units, etc. Does this make any sense?

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.